Skip to content

Commit

Permalink
Fix IRI duplication
Browse files Browse the repository at this point in the history
  • Loading branch information
@sebastianduesing
sebastianduesing committed Oct 9, 2024
1 parent 9a79b62 commit 69bfe36
Show file tree
Hide file tree
Showing 2 changed files with 83 additions and 1 deletion.
82 changes: 82 additions & 0 deletions src/ontology/modules/biobank-specimens.owl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1056,6 +1056,66 @@



<!-- http://purl.obolibrary.org/obo/OBI_0002123 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0002123"/>



<!-- http://purl.obolibrary.org/obo/OBI_0002124 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0002124"/>



<!-- http://purl.obolibrary.org/obo/OBI_0002125 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0002125">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OMIABIS_0000052"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0002124"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<obo:IAO_0000111>H&amp;E-stained fixed tissue slide specimen</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">A fixed tissue slide specimen that is the output of H&amp;E slide staining.</obo:IAO_0000115>
<obo:IAO_0000117>Chris Stoeckert, Ned Haubein</obo:IAO_0000117>
<obo:IAO_0000119>OBIB, OBI</obo:IAO_0000119>
<rdfs:label>H&amp;E-stained fixed tissue slide specimen</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/OBI_0002126 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0002126">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OMIABIS_0000052"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0002123"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<obo:IAO_0000111>IHC-stained fixed tissue slide specimen</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">A fixed tissue slide specimen that is the output of immunohistochemistry slide staining.</obo:IAO_0000115>
<obo:IAO_0000117>Chris Stoeckert, Ned Haubein</obo:IAO_0000117>
<obo:IAO_0000119>OBIB, OBI</obo:IAO_0000119>
<rdfs:label>IHC-stained fixed tissue slide specimen</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/OBI_0002127 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0002127">
Expand Down Expand Up @@ -4876,6 +4936,22 @@



<!-- http://purl.obolibrary.org/obo/OBI_1200000 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_1200000">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000950"/>
<obo:IAO_0000111>FFPE specimen</obo:IAO_0000111>
<obo:IAO_0000112>Many of today’s researchers prefer to use Formalin-Fixed Paraffin-Embedded samples of tissues for their IHC, histological or in-situ genomic analyses. Professionally fixed and embedded FFPE samples and the biomolecules they contain are reasonably stable at ambient temperatures. -based on https://lab-ally.com/histopathology-resources/ffpe-samples/</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">A specimen that has been fixed in formalin and embedded in paraffin.</obo:IAO_0000115>
<obo:IAO_0000117>MIABIS</obo:IAO_0000117>
<obo:IAO_0000118>formalin-fixed paraffin-embeded specimen</obo:IAO_0000118>
<obo:IAO_0000119>https://www.biochain.com/general/what-is-ffpe-tissue/</obo:IAO_0000119>
<obo:IAO_0000233>https://github.com/obi-ontology/obi/issues/1019</obo:IAO_0000233>
<rdfs:label>FFPE specimen</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/OBI_2000000 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_2000000">
Expand Down Expand Up @@ -5640,6 +5716,12 @@



<!-- http://purl.obolibrary.org/obo/OMIABIS_0000052 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OMIABIS_0000052"/>



<!-- http://purl.obolibrary.org/obo/PATO_0001421 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PATO_0001421"/>
Expand Down
2 changes: 1 addition & 1 deletion src/ontology/templates/biobank-specimens.tsv
View file
Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ OBI:0001472 specimen with known storage state specimen with known storage state
OBI:0001479 specimen from organism ready for release tissue specimen A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm). MO_954 organism_part PERSON: Chris Stoeckert, Jie Zheng equivalent specimen ('organism' or 'material anatomical entity' or 'anatomical cluster')
OBI:0001506 specimen with pre- or post-mortem status specimen with pre- or post-mortem status metadata complete A specimen that has been established to be taken from a live (pre-mortem) or dead (post-mortem) organism. MO_84 OrganismStatus PERSON: Chris Stoeckert, Jie Zheng organizational term, used in description of specimen that is created from known pre- or post-mortem status equivalent specimen ('organism' and ('has quality' some ('alive' or 'dead')))
OBI:0002125 H&E-stained fixed tissue slide specimen H&E-stained fixed tissue slide specimen pending final vetting A fixed tissue slide specimen that is the output of H&E slide staining. OBIB, OBI Chris Stoeckert, Ned Haubein equivalent fixed tissue slide specimen H&E slide staining
OBI:0002125 IHC-stained fixed tissue slide specimen IHC-stained fixed tissue slide specimen pending final vetting A fixed tissue slide specimen that is the output of immunohistochemistry slide staining. OBIB, OBI Chris Stoeckert, Ned Haubein equivalent fixed tissue slide specimen IHC slide staining
OBI:0002126 IHC-stained fixed tissue slide specimen IHC-stained fixed tissue slide specimen pending final vetting A fixed tissue slide specimen that is the output of immunohistochemistry slide staining. OBIB, OBI Chris Stoeckert, Ned Haubein equivalent fixed tissue slide specimen IHC slide staining
OBI:0002127 single cell specimen metadata complete A cell specimen that contains only one cell. PERSON: Jie Zheng, Alexander Diehl PERSON: Jie Zheng, Alexander Diehl Requested by Sirarat Sarntivijai (EBI). Details see tracker: https://sourceforge.net/p/obi/obi-terms/828/ subclass cell specimen
OBI:0002500 amniotic fluid specimen ready for release A specimen that is derived from amniotic fluid. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism collecting specimen from organism amniotic fluid UBERON_0000173
OBI:0002501 bile specimen ready for release A specimen that is derived from bile. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism collecting specimen from organism bile UBERON_0001970
Expand Down

0 comments on commit 69bfe36

Please sign in to comment.